Multiple sequence alignment - TraesCS3B01G195900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G195900 chr3B 100.000 3589 0 0 1 3589 222317218 222320806 0.000000e+00 6628
1 TraesCS3B01G195900 chr3D 94.491 2614 81 23 615 3215 151901144 151903707 0.000000e+00 3971
2 TraesCS3B01G195900 chr3D 92.619 569 18 8 12 566 151900104 151900662 0.000000e+00 797
3 TraesCS3B01G195900 chr3D 93.750 384 17 2 3212 3589 151904076 151904458 1.450000e-158 569
4 TraesCS3B01G195900 chr3A 93.844 2258 76 24 762 2995 178987753 178985535 0.000000e+00 3341
5 TraesCS3B01G195900 chr3A 92.543 751 33 7 12 752 178988904 178988167 0.000000e+00 1055
6 TraesCS3B01G195900 chr3A 94.574 645 18 6 2960 3589 178985527 178984885 0.000000e+00 981
7 TraesCS3B01G195900 chr5D 89.681 407 41 1 1235 1641 442331794 442332199 5.310000e-143 518
8 TraesCS3B01G195900 chr5B 89.681 407 41 1 1235 1641 538542401 538542806 5.310000e-143 518
9 TraesCS3B01G195900 chr4D 89.209 417 41 4 1227 1641 433393666 433393252 5.310000e-143 518
10 TraesCS3B01G195900 chr4B 89.346 413 43 1 1229 1641 531580995 531580584 5.310000e-143 518
11 TraesCS3B01G195900 chr4A 89.552 402 42 0 1240 1641 34787858 34787457 8.890000e-141 510
12 TraesCS3B01G195900 chr5A 88.943 407 44 1 1235 1641 558543699 558544104 5.350000e-138 501
13 TraesCS3B01G195900 chr6D 88.060 402 45 3 1239 1637 332499020 332499421 1.170000e-129 473


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G195900 chr3B 222317218 222320806 3588 False 6628.000000 6628 100.000000 1 3589 1 chr3B.!!$F1 3588
1 TraesCS3B01G195900 chr3D 151900104 151904458 4354 False 1779.000000 3971 93.620000 12 3589 3 chr3D.!!$F1 3577
2 TraesCS3B01G195900 chr3A 178984885 178988904 4019 True 1792.333333 3341 93.653667 12 3589 3 chr3A.!!$R1 3577

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
176 177 1.340889 TCATGTTTGGCACCTTTGAGC 59.659 47.619 0.00 0.00 0.00 4.26 F
208 209 1.448069 GGAGATCCTTTCCTCCGGC 59.552 63.158 0.00 0.00 39.49 6.13 F
497 520 1.544246 GGCGGCATAGTTGGTTCTTTT 59.456 47.619 3.07 0.00 0.00 2.27 F
1236 2096 1.080772 GGTCGATCGTGTGCACTGA 60.081 57.895 19.41 16.05 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1231 2091 0.320247 GTCAGGGTCTGCAGTCAGTG 60.320 60.000 14.67 9.29 41.10 3.66 R
1233 2093 1.080230 CGTCAGGGTCTGCAGTCAG 60.080 63.158 14.67 2.42 41.67 3.51 R
1835 2695 1.365633 GAGTATCTGCCCTCCTGCG 59.634 63.158 0.00 0.00 0.00 5.18 R
2886 3771 1.071857 TCAATTTGCCTGGCATTGCAA 59.928 42.857 24.03 14.21 45.12 4.08 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 6.642733 TGGTCCTTCAGATTTAAAGATCCT 57.357 37.500 0.00 0.00 0.00 3.24
87 88 6.206634 GGTTGATATCTTGTCTTGGTGTCAAA 59.793 38.462 3.98 0.00 31.77 2.69
171 172 5.772672 TGTAATACTTCATGTTTGGCACCTT 59.227 36.000 0.00 0.00 0.00 3.50
176 177 1.340889 TCATGTTTGGCACCTTTGAGC 59.659 47.619 0.00 0.00 0.00 4.26
191 192 5.418840 ACCTTTGAGCAATGTATTAAGGTGG 59.581 40.000 0.00 0.00 41.55 4.61
208 209 1.448069 GGAGATCCTTTCCTCCGGC 59.552 63.158 0.00 0.00 39.49 6.13
318 340 3.359033 TCAAGCATTCCAATCAAGGGAG 58.641 45.455 0.00 0.00 35.46 4.30
319 341 3.010472 TCAAGCATTCCAATCAAGGGAGA 59.990 43.478 0.00 0.00 35.46 3.71
497 520 1.544246 GGCGGCATAGTTGGTTCTTTT 59.456 47.619 3.07 0.00 0.00 2.27
845 1705 5.247564 TGGTATTGTTGCTTCCACTACTAGT 59.752 40.000 0.00 0.00 0.00 2.57
961 1821 4.024133 CGACCAACAACAACAATCTCATCA 60.024 41.667 0.00 0.00 0.00 3.07
977 1837 3.854666 TCATCAAGAGCTAGCAAGACAC 58.145 45.455 18.83 0.99 0.00 3.67
978 1838 2.751166 TCAAGAGCTAGCAAGACACC 57.249 50.000 18.83 0.00 0.00 4.16
979 1839 1.970640 TCAAGAGCTAGCAAGACACCA 59.029 47.619 18.83 0.00 0.00 4.17
980 1840 2.368548 TCAAGAGCTAGCAAGACACCAA 59.631 45.455 18.83 0.00 0.00 3.67
981 1841 2.740981 CAAGAGCTAGCAAGACACCAAG 59.259 50.000 18.83 0.00 0.00 3.61
1140 2000 2.277084 GGCACACCAGGTAATAAGTCG 58.723 52.381 0.00 0.00 35.26 4.18
1141 2001 2.354403 GGCACACCAGGTAATAAGTCGT 60.354 50.000 0.00 0.00 35.26 4.34
1142 2002 2.928116 GCACACCAGGTAATAAGTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
1144 2004 3.056393 CACACCAGGTAATAAGTCGTCCA 60.056 47.826 0.00 0.00 0.00 4.02
1145 2005 3.579586 ACACCAGGTAATAAGTCGTCCAA 59.420 43.478 0.00 0.00 0.00 3.53
1146 2006 4.224370 ACACCAGGTAATAAGTCGTCCAAT 59.776 41.667 0.00 0.00 0.00 3.16
1227 2087 2.260434 CAACCGGTGGTCGATCGT 59.740 61.111 8.52 0.00 42.43 3.73
1228 2088 2.092291 CAACCGGTGGTCGATCGTG 61.092 63.158 8.52 0.00 42.43 4.35
1229 2089 2.567497 AACCGGTGGTCGATCGTGT 61.567 57.895 8.52 0.00 42.43 4.49
1231 2091 3.179265 CGGTGGTCGATCGTGTGC 61.179 66.667 15.94 4.62 42.43 4.57
1232 2092 2.048597 GGTGGTCGATCGTGTGCA 60.049 61.111 15.94 0.00 0.00 4.57
1233 2093 2.380410 GGTGGTCGATCGTGTGCAC 61.380 63.158 15.94 10.75 0.00 4.57
1234 2094 1.372997 GTGGTCGATCGTGTGCACT 60.373 57.895 19.41 0.00 0.00 4.40
1235 2095 1.372872 TGGTCGATCGTGTGCACTG 60.373 57.895 19.41 10.84 0.00 3.66
1236 2096 1.080772 GGTCGATCGTGTGCACTGA 60.081 57.895 19.41 16.05 0.00 3.41
1718 2578 2.571757 CTCACGGCCGCTAGTTCA 59.428 61.111 28.58 0.00 0.00 3.18
2332 3192 3.984732 GGGGGCCTTTGAGCAGGT 61.985 66.667 0.84 0.00 36.15 4.00
2336 3196 2.282745 GCCTTTGAGCAGGTGCCT 60.283 61.111 0.00 0.00 43.38 4.75
2574 3440 2.924029 GCGCTCTGCTCATCATCGATAA 60.924 50.000 0.00 0.00 41.73 1.75
2579 3445 3.999001 TCTGCTCATCATCGATAAATGGC 59.001 43.478 15.97 16.69 0.00 4.40
2599 3465 3.381590 GGCTGGATTTAGTTTAAGCCTGG 59.618 47.826 4.28 0.00 45.42 4.45
2600 3466 3.181486 GCTGGATTTAGTTTAAGCCTGGC 60.181 47.826 11.65 11.65 34.68 4.85
2601 3467 4.016444 CTGGATTTAGTTTAAGCCTGGCA 58.984 43.478 22.65 0.00 34.68 4.92
2614 3480 1.601162 GCCTGGCATGCATGTTAATCG 60.601 52.381 26.79 11.44 0.00 3.34
2651 3517 4.866508 ACGAGGAGTAGTGTTTCATGAA 57.133 40.909 3.38 3.38 0.00 2.57
2662 3528 0.322098 TTTCATGAACCATCCGCGGT 60.322 50.000 27.15 10.00 42.71 5.68
2800 3673 8.377681 GCACATCATTCATGATTTTGTTACTTG 58.622 33.333 0.00 0.00 44.70 3.16
2801 3674 9.414295 CACATCATTCATGATTTTGTTACTTGT 57.586 29.630 0.00 0.00 44.70 3.16
2817 3698 9.787435 TTGTTACTTGTAGTACTTGATGGAATT 57.213 29.630 0.00 0.00 28.93 2.17
2886 3771 3.265221 TGGAGAAGATCTGAAGCAATGGT 59.735 43.478 0.00 0.00 0.00 3.55
2909 3794 2.352388 CAATGCCAGGCAAATTGAAGG 58.648 47.619 20.84 0.00 43.62 3.46
2911 3796 0.178938 TGCCAGGCAAATTGAAGGGA 60.179 50.000 13.33 0.00 34.76 4.20
2944 3829 4.082190 GCAAGAGATCCATGCATGCATATT 60.082 41.667 31.73 19.12 39.81 1.28
2945 3830 5.641709 CAAGAGATCCATGCATGCATATTC 58.358 41.667 31.73 25.12 34.91 1.75
2946 3831 4.918588 AGAGATCCATGCATGCATATTCA 58.081 39.130 31.73 16.20 34.91 2.57
2947 3832 4.944317 AGAGATCCATGCATGCATATTCAG 59.056 41.667 31.73 18.92 34.91 3.02
2948 3833 4.918588 AGATCCATGCATGCATATTCAGA 58.081 39.130 31.73 21.71 34.91 3.27
2949 3834 5.510430 AGATCCATGCATGCATATTCAGAT 58.490 37.500 31.73 24.74 34.91 2.90
2950 3835 6.659824 AGATCCATGCATGCATATTCAGATA 58.340 36.000 31.73 11.61 34.91 1.98
2951 3836 7.290813 AGATCCATGCATGCATATTCAGATAT 58.709 34.615 31.73 20.65 34.91 1.63
3052 3982 5.189180 AGAACCATTGATCAAAGAGTAGCC 58.811 41.667 13.09 4.13 0.00 3.93
3156 4091 2.898729 TTCAGTGCAGCTAGCTATCC 57.101 50.000 18.86 9.50 45.94 2.59
3239 4546 4.104897 AGGAGGATCTTTGCCCCTAATAAC 59.895 45.833 0.00 0.00 33.73 1.89
3289 4596 4.159321 TGTGCTTGTCCAAATGTCAAAGAA 59.841 37.500 0.00 0.00 0.00 2.52
3340 4647 4.159557 ACTTGAAACATAGCAATGGGGTT 58.840 39.130 0.00 0.00 37.43 4.11
3418 4725 2.298163 CTGTTTTGAATGGCTGCCTTCT 59.702 45.455 21.03 3.69 0.00 2.85
3428 4735 4.307032 TGGCTGCCTTCTAGATCTTTTT 57.693 40.909 21.03 0.00 0.00 1.94
3429 4736 5.435686 TGGCTGCCTTCTAGATCTTTTTA 57.564 39.130 21.03 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.259609 TCGTTAATGTCGGTCCCACT 58.740 50.000 0.00 0.00 0.00 4.00
1 2 2.159142 AGATCGTTAATGTCGGTCCCAC 60.159 50.000 0.00 0.00 38.94 4.61
2 3 2.100252 GAGATCGTTAATGTCGGTCCCA 59.900 50.000 0.00 0.00 38.94 4.37
3 4 2.100252 TGAGATCGTTAATGTCGGTCCC 59.900 50.000 0.00 0.00 38.94 4.46
4 5 3.431922 TGAGATCGTTAATGTCGGTCC 57.568 47.619 0.00 0.00 38.94 4.46
5 6 4.863131 AGTTTGAGATCGTTAATGTCGGTC 59.137 41.667 0.00 0.00 38.51 4.79
6 7 4.817517 AGTTTGAGATCGTTAATGTCGGT 58.182 39.130 0.00 0.00 30.21 4.69
7 8 5.779806 AAGTTTGAGATCGTTAATGTCGG 57.220 39.130 0.00 0.00 30.21 4.79
8 9 6.015504 CCAAAGTTTGAGATCGTTAATGTCG 58.984 40.000 17.33 0.00 30.21 4.35
9 10 6.899114 ACCAAAGTTTGAGATCGTTAATGTC 58.101 36.000 17.33 0.00 0.00 3.06
10 11 6.072673 GGACCAAAGTTTGAGATCGTTAATGT 60.073 38.462 17.33 1.58 0.00 2.71
53 54 9.219603 CAAGACAAGATATCAACCTTCTTTGTA 57.780 33.333 5.32 0.00 0.00 2.41
87 88 1.217882 CGTGCTCGTGAAGAAAGGTT 58.782 50.000 0.00 0.00 0.00 3.50
171 172 6.061022 TCTCCACCTTAATACATTGCTCAA 57.939 37.500 0.00 0.00 0.00 3.02
176 177 7.229506 GGAAAGGATCTCCACCTTAATACATTG 59.770 40.741 0.00 0.00 45.55 2.82
845 1705 3.696051 GGGCATCACTCAAGCAATCTAAA 59.304 43.478 0.00 0.00 0.00 1.85
961 1821 2.873649 GCTTGGTGTCTTGCTAGCTCTT 60.874 50.000 17.23 0.00 0.00 2.85
977 1837 0.538057 TGTGCTCCTTCTTGGCTTGG 60.538 55.000 0.00 0.00 35.26 3.61
978 1838 1.321474 TTGTGCTCCTTCTTGGCTTG 58.679 50.000 0.00 0.00 35.26 4.01
979 1839 2.299326 ATTGTGCTCCTTCTTGGCTT 57.701 45.000 0.00 0.00 35.26 4.35
980 1840 3.439857 TTATTGTGCTCCTTCTTGGCT 57.560 42.857 0.00 0.00 35.26 4.75
981 1841 3.181483 CCATTATTGTGCTCCTTCTTGGC 60.181 47.826 0.00 0.00 35.26 4.52
1063 1923 3.124921 GTGTTCATGGGACGGCGG 61.125 66.667 13.24 0.00 0.00 6.13
1064 1924 3.124921 GGTGTTCATGGGACGGCG 61.125 66.667 4.80 4.80 0.00 6.46
1065 1925 2.750237 GGGTGTTCATGGGACGGC 60.750 66.667 0.00 0.00 0.00 5.68
1140 2000 5.105837 GGGGATATACGTACTGAGATTGGAC 60.106 48.000 0.00 0.00 0.00 4.02
1141 2001 5.014858 GGGGATATACGTACTGAGATTGGA 58.985 45.833 0.00 0.00 0.00 3.53
1142 2002 5.017490 AGGGGATATACGTACTGAGATTGG 58.983 45.833 0.00 0.00 0.00 3.16
1144 2004 4.463186 GCAGGGGATATACGTACTGAGATT 59.537 45.833 11.56 0.00 0.00 2.40
1145 2005 4.017808 GCAGGGGATATACGTACTGAGAT 58.982 47.826 11.56 0.00 0.00 2.75
1146 2006 3.181437 TGCAGGGGATATACGTACTGAGA 60.181 47.826 11.56 0.00 0.00 3.27
1231 2091 0.320247 GTCAGGGTCTGCAGTCAGTG 60.320 60.000 14.67 9.29 41.10 3.66
1232 2092 1.810606 CGTCAGGGTCTGCAGTCAGT 61.811 60.000 14.67 0.00 41.10 3.41
1233 2093 1.080230 CGTCAGGGTCTGCAGTCAG 60.080 63.158 14.67 2.42 41.67 3.51
1234 2094 3.051210 CGTCAGGGTCTGCAGTCA 58.949 61.111 14.67 0.00 0.00 3.41
1235 2095 2.433318 GCGTCAGGGTCTGCAGTC 60.433 66.667 14.67 8.19 0.00 3.51
1236 2096 4.363990 CGCGTCAGGGTCTGCAGT 62.364 66.667 14.67 0.00 0.00 4.40
1763 2623 1.403687 GCCTGGCGAAGAGGTATCCT 61.404 60.000 1.35 0.00 36.03 3.24
1834 2694 2.093537 GAGTATCTGCCCTCCTGCGG 62.094 65.000 0.00 0.00 39.04 5.69
1835 2695 1.365633 GAGTATCTGCCCTCCTGCG 59.634 63.158 0.00 0.00 0.00 5.18
1838 2698 1.834822 GCCGAGTATCTGCCCTCCT 60.835 63.158 0.00 0.00 39.63 3.69
2324 3184 1.888436 CGGAGTTAGGCACCTGCTCA 61.888 60.000 18.50 0.00 41.70 4.26
2555 3421 4.093115 CCATTTATCGATGATGAGCAGAGC 59.907 45.833 19.34 0.00 0.00 4.09
2574 3440 5.598416 GGCTTAAACTAAATCCAGCCATT 57.402 39.130 3.07 0.00 45.29 3.16
2579 3445 4.016444 TGCCAGGCTTAAACTAAATCCAG 58.984 43.478 14.15 0.00 0.00 3.86
2596 3462 2.097954 ACACGATTAACATGCATGCCAG 59.902 45.455 26.53 13.82 0.00 4.85
2597 3463 2.090760 ACACGATTAACATGCATGCCA 58.909 42.857 26.53 11.62 0.00 4.92
2599 3465 4.035017 GGTTACACGATTAACATGCATGC 58.965 43.478 26.53 11.82 34.17 4.06
2600 3466 4.201773 ACGGTTACACGATTAACATGCATG 60.202 41.667 25.09 25.09 34.17 4.06
2601 3467 3.936453 ACGGTTACACGATTAACATGCAT 59.064 39.130 0.00 0.00 34.17 3.96
2614 3480 2.223433 CCTCGTATCTCCACGGTTACAC 60.223 54.545 0.00 0.00 42.19 2.90
2800 3673 7.681939 TGGTTCAAATTCCATCAAGTACTAC 57.318 36.000 0.00 0.00 0.00 2.73
2801 3674 8.877864 AATGGTTCAAATTCCATCAAGTACTA 57.122 30.769 0.00 0.00 42.73 1.82
2835 3716 5.249852 AGGTTAAGTTCCACTGGCACTAATA 59.750 40.000 0.28 0.00 0.00 0.98
2886 3771 1.071857 TCAATTTGCCTGGCATTGCAA 59.928 42.857 24.03 14.21 45.12 4.08
2894 3779 3.767902 TTTTCCCTTCAATTTGCCTGG 57.232 42.857 0.00 0.00 0.00 4.45
2909 3794 1.995376 TCTCTTGCCACCCTTTTTCC 58.005 50.000 0.00 0.00 0.00 3.13
2911 3796 2.158325 TGGATCTCTTGCCACCCTTTTT 60.158 45.455 0.00 0.00 0.00 1.94
2944 3829 8.774546 AGACCATAGTTCTTGAGAATATCTGA 57.225 34.615 0.00 0.00 36.33 3.27
2950 3835 9.432982 AGAAGATAGACCATAGTTCTTGAGAAT 57.567 33.333 0.00 0.00 36.33 2.40
2951 3836 8.830915 AGAAGATAGACCATAGTTCTTGAGAA 57.169 34.615 0.00 0.00 0.00 2.87
3052 3982 8.857694 TGAGACAAAGTAATAAACTAAAGGGG 57.142 34.615 0.00 0.00 37.50 4.79
3156 4091 7.558161 TGTTCAAACAGGATCAAGCTATATG 57.442 36.000 0.00 0.00 34.30 1.78
3257 4564 6.015180 ACATTTGGACAAGCACAACAAGATAT 60.015 34.615 0.00 0.00 0.00 1.63
3289 4596 1.615384 GGGCTTGCTTGAACCTCAGAT 60.615 52.381 0.00 0.00 0.00 2.90
3340 4647 6.069323 TCCTTATTGTTGCTAGGTTATTGGGA 60.069 38.462 0.00 0.00 0.00 4.37
3429 4736 8.296713 CGCACCACTGGCTAATTATTAATAAAT 58.703 33.333 11.80 6.51 0.00 1.40
3510 4818 6.952773 TTACAACCAAAATGCACTAAGAGT 57.047 33.333 0.00 0.00 0.00 3.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.